title: H3: siRNA-EZH2 3

city: Muenster

first: Carsten

last: Müller-Tidow

address: Domagkstr. 3

department: Department of Medicine, Hematology and Oncology

institute: University of Muenster

description:
siRNA-mediated downregulation of EZH2
ChIP performed with anti-H3
Chromatin immunoprecipitated DNA

hyb_protocol: After slide processing, dryed and labeled DNA was resuspended in 4 µl hCoT-DNA (Invitrogen). Preheated hybridisation buffer (25% Formamide; 5x SSC) was added. Hybridisation was performed for 24 h at 38°C

scan_protocol: Slides were scanned using an Axon 4000B scanner

data_processing: Scanned images were analysed with Spotreader software (Niles Scientific Inc.). Spots with aberrant morphology or those below the threshold of detection were flagged. The data analysis was performed with BRB Array Tool (National Cancer Institute). The Arrays were median centered.

label: Alexa dye 647nm

source_name: A673 cells

label_protocol: Immunoprecipitated DNA was amplified in duplicates (a + b)  using the WGA-Kit. 1 µg DNA of each sample was labeled with amino-allyl-conjugated dUTP using the BioPrime labelling kit (Invitrogen).Purified products were coupled with Alexa dye (647 nm).

extract_protocol: Formaldehyd fixed cells were lysed in RIPA containing a protease inhibitor mix and TSA. The samples were sonicated to an averange length of 500 bp. After immunoprecipitation the proteins were digested and the DNA was purified.

treatment_protocol: Cells were transistient transfected with siRNA-EZH2 and siRNA-scrambeled respectivly

tag: cell line


title: gDNA-4

status: Public on Jun 10 2009

type: genomic

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: The growth experiments and DNA extractions were preformed at the Technical University of Denmark. The cDNA synthesis, labelling, hybridization and scanning was performed at NimbleGen.

hyb_protocol: Hybridization was performed using a MAUI Hybridization System at 42C overnight using NimbleGen standard protocols. Washing was performed using NimbleGen Wash Buffer Kit according to manufacturers instructions.

scan_protocol: GenePix 4000B Scanner at 532 nm

data_processing: Normalized values were generated by normalizing the raw data with "Qspline" using R and Bioconductor (affy package). No background correction were used.

molecule: genomic DNA

source_name: Bacillus subtilis, mid-exponential growth in LB

label_protocol: Genomic DNA was fragmented using a Branson model 450 Sonifier to size range of ~500bp to 2,000bp. This was labelled using Klenow Enzyme and Cy3-labelled 9mer primers using NimbleGen standard protocols.

growth_protocol: Bacillus subtilis subsp. subtilis str. 168 grown in Luria-Broth medium at 37C, 120rpm. Cells harvested at OD600 = 0.5

extract_protocol: DNA was extracted using the DNeasy Blood tissue kit from Qiagen as recommended by the supplier from 2 mL culture at OD600 = 0.5.

tag: growth medium

value: Luria-Broth medium


title: M9-1

type: RNA

description: The growth experiments and RNA extractions were preformed at the Technical University of Denmark. The cDNA synthesis, labelling, hybridization and scanning was performed at NimbleGen.

hyb_protocol: Hybridization was performed using a MAUI Hybridization System at 42C overnight.

molecule: total RNA

source_name: Bacillus subtilis, mid-exponential growth in M9

label_protocol: For the reverse transcription reactions Invitrogen Superscript Double-Stranded cDNA Synthesis Kit was used and in the presence of 40 ug/mL Actinomycin D to prevent antisense artifacts. First strand cDNA were synthesised using random primers and each cDNA strand were labelled using Cy3 using Klenow Enzyme and Cy3-labelled 9-mer primers.

growth_protocol: Bacillus subtilis subsp. subtilis str. 168 grown in M9 minimal medium at 37C, 120rpm. Cells harvested at OD600 = 0.5

extract_protocol: A total of 25 mL from each culture was transferred to a 40 mL tube 1/3-filled with crushed ice and spun at 7,000 rpm for 5 minutes, after which the supernatant was discarded and the cell pellet frozen by dumping the closed tube into liquid nitrogen. Total RNA was extracted by the use of the FastRNA PRO Blue Kit from Qbiogene as recommended by the supplier, but with an additional shake in the FastPrep instrument and a one minute incubation on ice between the two shakings.

value: M9 minimal medium


title: H3: siRNA-EZH2 4

status: Public on Jun 02 2009

country: Germany

organism: Homo sapiens


title: H3K27me3: siRNA control 1

description:
use of scrambeled siRNA
ChIP performed with anti-H3K27
Chromatin immunoprecipitated DNA

label: Alexa dye 555nm

label_protocol: Immunoprecipitated DNA was amplified using the WGA-Kit. 1 µg DNA of each sample was labeled with amino-allyl-conjugated dUTP using the BioPrime labelling kit (Invitrogen).Purified products were coupled with Alexa dye (555nm)


title: H3: siRNA control 3

description:
use of scrambeled siRNA
ChIP performed with anti-H3
Chromatin immunoprecipitated DNA


title: H3: siRNA-control 1


title: H3: siRNA-EZH2 1


title: H3: siRNA-control 4


title: H3: siRNA-control 2


title: H3K27me3: siRNA-EZH2 2

description:
siRNA-mediated downregulation of EZH2
ChIP performed with anti-H3K27
Chromatin immunoprecipitated DNA


title: 26vs1.5 hyb_3

status: Public on Jun 01 2009

city: marseille cedex 9

first: Gwenola

last: Simon

address: 163 avenue de Luminy

department: ESIL case 925

country: France

institute: IRD

description: Biological replicate 3 of 3

hyb_protocol: Samples were mixed (17.4 µL total) with 42.6 µL of hybridization mix (45% formamide, 5X SSC, 0.1% SDS), 1 ml 10 mg/ml tRNA and 1 ml 10 mg/ml herring sperm DNA. The mixture was incubated 2 min at 95oC and then applied to prehybridized (1% BSA, 5X SSC, 0.1% SDS 40 min followed by 3X washes in water and 1X wash in isopropanol) microarrays. Slides were hybridized for 20 h at 42°C in hybridization cassettes (Array-It), washed 5 min, 2X SSC, 0.1% SDS at 42°C; 20 min, 0.1X SSC, 0.1% SDS at 42°C, then in five different Coplin jars at RT 0.1X SSC and dried.

scan_protocol: After hybridisation, the microarrays were scanned at a resolution of 5 mm with a Genepix 4000B scanner (Axon Instruments) using the appropriate laser and filter settings. Spots were analysed with the Genepix pro 6.0 software package (Axon Instruments).

data_processing: Low-quality spots were excluded using criteria that were previously described. 2Log-transformed ratios (2log(YT/G)) from the replicate slides were averaged after first averaging the duplicate spots on the array. Statistical significance for the observed ratios was calculated by doing a significance analysis of microarrays (SAM) analysis.

organism: Saccharolobus solfataricus

label_protocol: 15 µg of RNA, 5 µg of random hexamers was added in a total volume of 11.6 µL. This was incubated for 10 min at 70°C after which the mixture was cooled on ice. Next, dATP, dGTP and dCTP (5 µM final concentration) were added, together with 4 µM aminoallyl dUTP (Sigma), 1 µM dTTP, 10 mM DTT, 400 U superscript II (Invitrogen) and the corresponding 5xRT buffer in a final volume of 20 µL. The reverse transcriptase reaction was carried out at 42°C for 1 h. To stop the reaction and to degrade the RNA, 2 µL 200 mM EDTA and 3 µL 1 M NaOH were added to the reaction mixture, after which it was incubated at 70°C for 15 min. After neutralisation by the addition of 3 µL 1 M HCl, the cDNA was purified using a Qiagen MinElute kit according to the manufacturer, except that the wash buffer was replaced with 80% v/v ethanol. The cDNA was then labelled using postlabelling reactive CyDye packs (Amersham Biosciences), according to the protocol provided by the company. Excess label was removed by cDNA purification using the MinElute kit.

growth_protocol: S. solfataricus P2 cells (DSM 1617) were grown at 80 °C and pH=3 on Brock medium, in Penicillin bottles (500 ml with 50-ml medium), sealed with Teflon-coated rubber stoppers. The settings for N2 and O2 flows were calculated in order to reach 1.5% O2 in the headspace (in volume percentage).

extract_protocol: Total RNA was isolated from S. solfataricus using the RNeasy method (QIAgen). 50 ml of Early-log phase culture (A600 of 0.3) was washed in 1 ml of medium and resuspended in 100 µl of TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). 5 µl of 10% Triton X-100 was added, and further purification was done according the manufacturer’s prescriptions, except that genomic DNA was sheared through a 0.45-mm needle before the sample was applied onto the column. Columns were eluted twice with 50 µl of water.

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing 1.5% O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.

tag: strain

value: Sulfolobus solfataricus P2

growth_protocol: S. solfataricus P2 cells (DSM 1617) were grown at 80 °C and pH=3 on Brock medium, in Penicillin bottles (500 ml with 50-ml medium), sealed with Teflon-coated rubber stoppers. The settings for N2 and O2 flows were calculated in order to reach 26% O2 in the headspace (in volume percentage).

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing 26% O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.


title: gDNA-2

organism: Bacillus subtilis subsp. subtilis str. 168


title: H3K27me3: siRNA-control 2


title: H3K27me3: siRNA-EZH2 1


title: H3: siRNA-EZH2 2


title: gDNA-1


title: 26vs1.5 hyb_2

description: Biological replicate 2 of 3


title: 1.5vs26 hyb_3

description: Biological replicate 3 of 3


title: 26vs1.5 hyb_1

description: Biological replicate 1 of 3


title: 1.5vs21 hyb_3

description: Biological replicate 3 of 3

growth_protocol: S. solfataricus P2 cells (DSM 1617) were grown at 80 °C and pH=3 on Brock medium, in Penicillin bottles (500 ml with 50-ml medium), sealed with Teflon-coated rubber stoppers. The settings for N2 and O2 flows were calculated in order to reach 21% O2 in the headspace (in volume percentage).

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing  21 % O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing 1,5 % O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.


title: 21vs1.5 hyb_3

description: Biological replicate 3 of 3

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing 21 % O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.


title: 21vs1.5 hyb_1

description: Biological replicate 1 of 3


title: 1.5vs26 hyb_2

description: Biological replicate 2 of 3


title: 21vs1.5 hyb_2

description: Biological replicate 2 of 3


title: 1.5vs21 hyb_1

description: Biological replicate 1 of 3

treatment_protocol: Samples (50 ml), taken from cultures at OD600nm=0.3 containing 1,5 %, 10 %, 21 % or 26 % O2 in the gas phase, were centrifuged and snap-frozen in liquid N2.


title: 1.5vs26 hyb_1

description: Biological replicate 1 of 3


title: 1.5vs21 hyb_2

description: Biological replicate 2 of 3


title: Total breast tumor_ adriamycin _07SE144

city: Granada

first: Sergio

last: Granados

address: Avenida del Conocimiento

country: Spain

institute: University of Granada

description: Affymetrix standard protocols

hyb_protocol: Affymetrix GeneChip Hybridization standard protocol

scan_protocol: Affymetrix GeneChip scan standard protocol

data_processing: Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.

label: Biotin

organism: Rattus norvegicus

source_name: Total breast tumor, adriamycin, final moment

label_protocol: Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)

treatment_protocol: RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction protocol

value: Sprague-Dawley

tag: gender

value: female

tag: age

value: 19 weeks

tag: tissue

value: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.

tag: treatment

value: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy.

tag: sacrifice

value: 7th week post-biopsy

tag: sample

value: 43D1 (final)


title: Total breast tumor_ adriamycin _07SE142

description: Affymetrix standard protocols

value: 12I1 (final)


title: Total breast tumor_ adriamycin _07SE141

description: Affymetrix standard protocols

value: 11D2 (final)


title: Breast tumor biopsy_adriamycin_07SE127

description: Affymetrix standard protocols

source_name: Breast tumor biopsy, adriamycin, basal moment

value: 12 weeks

value: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume.

tag: biopsy dimensions

value: 12I1 (basal)


title: Total breast tumor_ adriamycin _07SE143

description: Affymetrix standard protocols

value: 29I1 (final)


title: Breast tumor biopsy_adriamycin_07SE126

description: Affymetrix standard protocols

value: 11D2 (basal)


title: Total breast tumor_hydroxytyrosol_07SE136

description: Affymetrix standard protocols

source_name: Total breast tumor, hydroxytyrosol, final moment

value: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.

value: 67D3 (final)


title: Breast tumor biopsy_hydroxytyrosol_07SE121

description: Affymetrix standard protocols

source_name: Breast tumor biopsy, hydroxytyrosol, basal moment

value: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume


title: Total breast tumor_ adriamycin _07SE140

description: Affymetrix standard protocols

value: Sprague-Dawley

value: 09I1 (final)


title: Breast tumor biopsy_hydroxytyrosol_07SE123

description: Affymetrix standard protocols

value: female

value: 49I1 (basal)


title: Total breast tumor_hydroxytyrosol_07SE139

description: Affymetrix standard protocols

value: 19 weeks

value: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.

value: 51I1 (final)


title: Breast tumor biopsy_adriamycin_07SE128

description: Affymetrix standard protocols

value: 29I1 (basal)


title: Breast tumor biopsy_adriamycin_07SE125

description: Affymetrix standard protocols

value: 09I1 (basal)


title: Breast tumor biopsy_hydroxytyrosol_07SE122

description: Affymetrix standard protocols

value: 12 weeks

value: 45D3 (basal)


title: Breast tumor biopsy_adriamycin_07SE129

description: Affymetrix standard protocols

value: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume.

value: 43D1 (basal)


title: Breast tumor biopsy_hydroxytyrosol_07SE124

description: Affymetrix standard protocols

value: 51I1 (basal)


title: Breast tumor biopsy_hydroxytyrosol_07SE120

description: Affymetrix standard protocols

value: 66D2 (basal)


title: Total breast tumor_hydroxytyrosol_07SE135

description: Affymetrix standard protocols

value: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.

value: 7th week post-biopsy

value: 66D2 (final)


title: Total breast tumor_hydroxytyrosol_07SE138

description: Affymetrix standard protocols

value: Sprague-Dawley

value: 49I1 (final)


title: Total breast tumor_hydroxytyrosol_07SE137

description: Affymetrix standard protocols

value: female

value: 45D3 (final)


title: Total breast tumor_DMBA_07SE134

description: Affymetrix standard protocols

source_name: Total breast tumor, DMBA, final moment

treatment_protocol: RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.

value: 19 weeks

value: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.


title: Breast tumor biopsy_DMBA_07SE119

description: Affymetrix standard protocols

source_name: Breast tumor biopsy, DMBA, basal moment

value: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.

value: 52I4 (basal)


title: Total breast tumor_DMBA_07SE133

description: Affymetrix standard protocols

value: 50I1 (final)


title: Total breast tumor_DMBA_07SE131

description: Affymetrix standard protocols

value: 32D1 (final)


title: Total breast tumor_DMBA_07SE132

description: Affymetrix standard protocols

value: 37I1 (final)


title: AML sample #96

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

country: USA

institute: Columbia University Medical Center

description: de novo AML, NPM1 mutated, normal karyotype

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.20.2) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Samples are from untreated patients (de novo AML)

value: 2-positive (mutated)

tag: karyotype

value: normal karyotype


title: Breast tumor biopsy_DMBA_07SE116

description: Affymetrix standard protocols

value: 12 weeks

value: 32D1 (basal)


title: AML sample #91


title: Breast tumor biopsy_DMBA_07SE118

description: Affymetrix standard protocols

value: 50I1 (basal)


title: Breast tumor biopsy_DMBA_07SE115

description: Affymetrix standard protocols

value: 31D3 (basal)


title: AML sample #92


title: AML sample #83


title: AML sample #84


title: AML sample #81


title: AML sample #93


title: AML sample #89


title: AML sample #85


title: AML sample #94


title: Total breast tumor_DMBA_07SE130

description: Affymetrix standard protocols

value: Sprague-Dawley

value: 31D3 (final)


title: AML sample #82


title: AML sample #87


title: AML sample #95


title: AML sample #90


title: AML sample #86


title: AML sample #88


title: AML sample #97


title: AML sample #78


title: AML sample #77


title: AML sample #40

description: de novo AML, NPM1 wild type, normal karyotype

value: 1-negative (wild type)


title: AML sample #41


title: AML sample #80


title: AML sample #34


title: AML sample #42


title: AML sample #30


title: AML sample #29


title: AML sample #28


title: AML sample #35


title: P13 neocortex 3

status: Public on May 30 2009

first: Sung Wook

last: Chi

address: 1230 York Ave,

institute: Rockefeller Univ

description: Expression analysis.

hyb_protocol: Affymetrix WT Sense Target Labeling Assay.

scan_protocol: The scanning and image acquisition was done using Affymetrix GeneChip Operating Software (GCOS) v1.4. The scanner model is GeneChip Scanner 3000 7G.

data_processing:
Affymetrix Power Tools(Affymetrix); median normalization; PM-GCBG; iterPLIER.

Analysis was limited to core probe sets. Transcript assignments are based on genome build mm8 (NCBI Build 36).

label: biotin

organism: Mus musculus

source_name: wild type cortex

extract_protocol: Trizol Extraction.

value: brain

tag: brain region

value: cortex

tag: developmental stage


title: AML sample #38


title: P13 neocortex 2

description: Expression analysis.

label_protocol: Affymetrix WT Sense Target Labeling Assay.


title: AML sample #27


title: AML sample #31


title: AML sample #33


title: AML sample #36


title: AML sample #70


title: AML sample #37


title: AML sample #32


title: AML sample #39


title: Anti-CD3 + ALCAM + IL-2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

source_name: Human PBMC Cells

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA

extract_protocol: The whole of tissue was used for RNA isolation by using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.

treatment_protocol: 30000 freshly isolated  (Ficoll Paque) human unstimulated PBMCs cells (lane 5), incubated for 72 h at 37oC, 5% CO2.  Cells were maintained in RPMI 1640 supplemented with 10% FBS, 2mM L-Glutamine, 25mM HEPES, 1% 10000 units/ml of penicillin and 10000ug/ml of streptomycin

tag: cell type

value: peripheral blood mononuclear cell


title: P13 neocortex 1

description: Expression analysis.


title: PBMC Healthy Control INF 8N HG-U133B

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Healthy patient.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 System.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNEasy Mini Kit

value: 10y, when sample taken

value: Male

tag: race

value: Black

tag: illness

tag: pathogen


title: Anti-CD3 + ALCAM

treatment_protocol: 30000 freshly isolated (Ficoll Paque) human PBMCs cells stimulated with the immobilized anti-CD3 monoclonal antibody (iorT3) (0.25ug/ml) and Human Recombinant IL-2 (2.5ng/ml) (lane 4), incubated for 72 h at 37oC, 5% CO2.  Cells were maintained in RPMI 1640 supplemented with 10% FBS, 2mM L-Glutamine, 25mM HEPES, 1% 10000 units/ml of penicillin and 10000ug/ml of streptomycin


title: Anti-CD3

treatment_protocol: 30000 freshly isolated (Ficoll Paque)  human PBMCs cells stimulated with the immobilized anti-CD3 monoclonal antibody (iorT3) (0.25ug/ml), immobilized human ALCAM-Fc Chimera (1ug/ml) (lane 2), incubated for 72 h at 37oC, 5% CO2.  Cells were maintained in RPMI 1640 supplemented with 10% FBS, 2mM L-Glutamine, 25mM HEPES, 1% 10000 units/ml of penicillin and 10000ug/ml of streptomycin


title: PBMC S. aureus INF 90 HG-U133B

description: The subject was infected with Staphylococcus aureus, methicillin-susceptible.

value: 0.67y, when sample taken

value: Bacteremia, Suppurative arthritis

value: Anti-staphylococcal antibiotic


title: Anti-CD3 + IL-2

treatment_protocol: 30000 freshly isolated (Ficoll Paque) human PBMCs cells stimulated with the immobilized anti-CD3 monoclonal antibody (iorT3) (0.25ug/ml), immobilized human ALCAM-Fc Chimera (1ug/ml) and Human Recombinant IL-2 (2.5ng/ml) (lane 3), incubated for 72 h at 37oC, 5% CO2.  Cells were maintained in RPMI 1640 supplemented with 10% FBS, 2mM L-Glutamine, 25mM HEPES, 1% 10000 units/ml of penicillin and 10000ug/ml of streptomycin


title: PBMC S. aureus INF 67 HG-U133B

description: The subject was infected with Staphylococcus aureus, methicillin-resistant.

value: 7y, when sample taken

value: Female

value: White

value: Bacteremia, Osteomyelitis


title: PBMC S. aureus INF 450 HG-U133B

value: 0.83y, when sample taken

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Pyomyositis


title: PBMC S. aureus INF 88 HG-U133B

value: 0.92y, when sample taken

value: Hispanic

value: Bacteremia, Osteomyelitis, Pneumonia, Emboli


title: PBMC S. aureus INF 62 HG-U133B

value: 2y, when sample taken

value: Osteomyelitis, Pyomyositis


title: Pooled Control Sample - P1

extract_protocol: The whole of tissue was used for RNA isolation by   using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.

treatment_protocol: 30000 freshly isolated (Ficoll Paque) human PBMCs cells stimulated with the immobilized anti-CD3 monoclonal antibody  (iorT3) (0.25ug/ml) (lane 1), incubated for 72 h at 37oC, 5% CO2.  Cells were maintained in RPMI 1640 supplemented with 10% FBS, 2mM L-Glutamine, 25mM HEPES, 1% 10000 units/ml of penicillin and 10000ug/ml of streptomycin

value: peripheral blood mononuclear cell


title: PBMC S. aureus INF 440 HG-U133B

value: 0.5y, when sample taken

value: Male


title: PBMC Healthy Control INF 7N HG-U133B

description: Healthy patient.

value: 1.6y, when sample taken

value: Black


title: PBMC S. aureus INF 434 HG-U133B

value: 5y, when sample taken

value: Anti-staphylococcal antibiotic


title: PBMC S. aureus INF 423 HG-U133B

value: 8y, when sample taken

value: Bacteremia, Osteomyelitis, Pyomyositis


title: PBMC S. aureus INF 412 HG-U133B

value: 1.75y, when sample taken

value: White

value: Bacteremia, Suppurative Arthritis


title: PBMC S. aureus INF 66 HG-U133B

value: 0.25y, when sample taken

value: Female

value: Pneumonia


title: PBMC S. aureus INF 5 HG-U133B

value: 10y, when sample taken

value: Hispanic

value: Osteomyelitis


title: PBMC S. aureus INF 43 HG-U133B

value: 7y, when sample taken

value: Bacteremia, Osteomyelitis, Pyomyositis, Suppurative Arthritis, Emboli


title: PBMC S. aureus INF 418 HG-U133B


title: PBMC S. aureus INF 451 HG-U133B

value: 4y, when sample taken

value: Male

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Pyomyositis, Emboli


title: PBMC S. aureus INF 40 HG-U133B

value: 13y, when sample taken

value: Bacteremia, Osteomyelitis

value: Anti-staphylococcal antibiotic


title: PBMC S. aureus INF 372 HG-U133B

value: 14y, when sample taken

value: Bacteremia, Osteomyelitis, Myositis


title: PBMC S. aureus INF 328 HG-U133B

value: 0.38y, when sample taken

value: Black

value: Bacteremia, Osteomyelitis, Pneumonia, Skin/Soft Tissue Abscess


title: PBMC S. aureus INF 330 HG-U133B

value: 11y, when sample taken

value: Female

value: Bacteremia, Pneumonia


title: PBMC S. aureus INF 308 HG-U133B

value: 12y, when sample taken

value: Bacteremia, Pneumonia, Skin/Soft Tissue Abscess, Pyomyositis


title: PBMC S. aureus INF 369 HG-U133B

value: Bacteremia, Suppurative arthritis, Skin/Soft Tissue Abscess, Emboli


title: PBMC S. aureus INF 329 HG-U133B

value: 0.58y, when sample taken

value: Other

value: Bacteremia, Lymphadenitis


title: PBMC S. aureus INF 354 HG-U133B

value: 2y, when sample taken

value: Hispanic


title: PBMC S. aureus INF 305 HG-U133B

value: 4y, when sample taken

value: Bacteremia, Osteomyelitis, Suppurative Arthritis

value: Anti-staphylococcal antibiotic


title: PBMC S. aureus INF 366 HG-U133B

value: Osteomyelitis, Skin/Soft Tissue Abscess


title: PBMC Healthy Control INF 303 HG-U133B

description: Healthy patient.

value: 6y, when sample taken

value: White


title: PBMC S. aureus INF 30 HG-U133B

value: 15y, when sample taken

value: Male

value: Black

value: Bacteremia


title: PBMC S. aureus INF 330 HG-U133A

value: 11y, when sample taken

value: Female

value: Bacteremia, Pneumonia


title: 13190051 - Silique vs Silique Alone

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: WP3 : Biodiversity of seed traits : state of the art

hyb_protocol: Silique Alone Cy5 / Silique Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Silique Alone

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media : MS Hygrometry : 70% Temperature : 22 degree C day - 19 degree C night Light : 16h day - 8h night

extract_protocol: Silique :13.9ug.

treatment_protocol: no treatment

tag: ecotype

value: arabidopsis thaliana (bay0)

source_name: Silique


title: PBMC Healthy Control INF 294 HG-U133B

description: Healthy patient.

value: 12y, when sample taken


title: PBMC S. aureus INF 264 HG-U133B

value: 13y, when sample taken

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Myositis, Skin/Soft Tissue Abscess, Emboli


title: PBMC Healthy Control INF 301 HG-U133B

description: Healthy patient.

value: 8y, when sample taken


title: 13190048 - Seed vs Silique

hyb_protocol: Silique Cy5 / Seed Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Seed


title: PBMC Healthy Control INF 304 HG-U133B

description: Healthy patient.


title: PBMC S. aureus INF 262 HG-U133B

value: Hispanic

value: Bacteremia, Skin/Soft Tissue Abscess


title: AML sample #79

value: 2-positive (mutated)

value: normal karyotype


title: PBMC S. aureus INF 271 HG-U133B

value: Osteomyelitis, Pyomyositis

value: Anti-staphylococcal antibiotic


title: PBMC Healthy Control INF 3N HG-U133B

description: Healthy patient.

value: 6y, when sample taken

value: Male


title: 13190052 - Silique Alone vs Silique

hyb_protocol: Silique Cy5 / Silique Alone Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13190045 - Silique vs Seed

hyb_protocol: Seed Cy5 / Silique Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 258 HG-U133B

value: White

value: Bacteremia, Osteomyelitis, Cellulitis


title: PBMC S. aureus INF 242 HG-U133B

value: 1.2y, when sample taken

value: Black

value: Bacteremia, Osteomyelitis, Pyomyositis


title: PBMC S. aureus INF 241 HG-U133B

value: 0.92y, when sample taken

value: Female

value: Bacteremia, Osteomyelitis, Pneumonia


title: 13281275 - Silique 10d vs Silique 8d

hyb_protocol: Silique 8d Cy5 / Silique 10d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Silique 8d

growth_protocol: silique and seed - Media : MS Hygrometry : 70% Temperature : 22 degree C day and 19 degree C night Light : 16h day and 8h night

extract_protocol: Silique 8d:12.1ug.

value: 8 day

value: arabidopsis thaliana (bay0)

source_name: Silique 10d

extract_protocol: Silique 10d:6.1ug.

value: 10 day


title: PBMC Healthy Control INF 301 HG-U133A

description: Healthy patient.

value: 8y, when sample taken


title: PBMC Healthy Control INF 24N HG-U133B

description: Healthy patient.

value: 3y, when sample taken


title: 13279357 - Silique 12d vs Silique 10d

hyb_protocol: Silique 10d Cy5 / Silique 12d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Silique 12d

extract_protocol: Silique 12d:4.3ug.

value: 12 day


title: 13301355 - Bay0 a vs Sha a

hyb_protocol: Sha a Cy5 / Bay0 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Sha a

growth_protocol: seed - Media: individual tray Hygrometry: 60% Temperature: day 22 degree C, night 20 degree C Light: 16h light (6h-22h), 8h dark

value: arabidopsis thaliana (shahdara)

tag: dev stage

value: (boyes et al. plant cell 2001):boyes:6.50

source_name: Bay0 a


title: 13279362 - Silique 14d vs Silique 12d

hyb_protocol: Silique 12d Cy5 / Silique 14d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Silique 14d

extract_protocol: Silique 14d:3.4ug.

value: 14 day


title: 13281274 - Silique 8d vs Silique 10d

hyb_protocol: Silique 10d Cy5 / Silique 8d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300942 - RIL 104 b vs RIL 140 b

hyb_protocol: RIL 140 b Cy5 / RIL 104 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 140 b

value: arabidopsis thaliana (ril bay-0 x shahdara)

source_name: RIL 104 b


title: 13190046 - Silique Alone vs Seed

hyb_protocol: Seed Cy5 / Silique Alone Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300940 - Bay0 b vs Sha b

hyb_protocol: Sha b Cy5 / Bay0 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Sha b

extract_protocol: Sha b:7.73ug.

source_name: Bay0 b


title: PBMC S. aureus INF 24 HG-U133B

value: Male

value: Bacteremia, Osteomyelitis, Myositis

value: Anti-staphylococcal antibiotic


title: 13190044 - Seed vs Silique Alone

hyb_protocol: Silique Alone Cy5 / Seed Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 230 HG-U133B

value: 20y, when sample taken

value: Black

value: Bacteremia, Endocarditis, Skin/Soft Tissue Abscess


title: 13301357 - Sha a vs Bay0 a

hyb_protocol: Bay0 a Cy5 / Sha a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC Healthy Control INF 23N HG-U133B

description: Healthy patient.

value: 7y, when sample taken

value: Female

value: Hispanic


title: 13279358 - Silique 12d vs Silique 14d

hyb_protocol: Silique 14d Cy5 / Silique 12d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (bay0)


title: 13300943 - RIL 140 b vs RIL 104 b

hyb_protocol: RIL 104 b Cy5 / RIL 140 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13279356 - Silique 10d vs Silique 12d

hyb_protocol: Silique 12d Cy5 / Silique 10d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 10 day


title: 13300941 - Sha b vs Bay0 b

hyb_protocol: Bay0 b Cy5 / Sha b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 224 HG-U133B

value: 10y, when sample taken

value: White

value: Bacteremia, Osteomyelitis


title: 13300938 - RIL 104 a vs RIL 140 a

hyb_protocol: RIL 140 a Cy5 / RIL 104 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 140  a

value: (boyes et al. plant cell 2001):boyes:6.50

source_name: RIL 104  a


title: 13300939 - RIL 140 a vs RIL 104 a

hyb_protocol: RIL 104 a Cy5 / RIL 140 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 221 HG-U133B

value: 6y, when sample taken


title: PBMC S. aureus INF 960 Illumina Human6

hyb_protocol: Human-6 BeadChip

scan_protocol: SentrixScanVersion 2.3.0.37

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

value: 3y, when sample taken

value: Pneumonia


title: 13300935 - RIL 140 a vs Sha a

hyb_protocol: Sha a Cy5 / RIL 140 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (shahdara)

value: arabidopsis thaliana (ril bay-0 x shahdara)


title: PBMC S. aureus INF 220 HG-U133B

value: 11y, when sample taken

value: Male

value: Anti-staphylococcal antibiotic


title: PBMC S. aureus INF 216 HG-U133B


title: 13300936 - Bay0 a vs RIL 104 a

hyb_protocol: RIL 104 a Cy5 / Bay0 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300937 - RIL 104 a vs Bay0 a

hyb_protocol: Bay0 a Cy5 / RIL 104 a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300747 - RIL 140 b vs Sha b

hyb_protocol: Sha b Cy5 / RIL 140 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 179 HG-U133B

value: 12y, when sample taken

value: Bacteremia, Endocarditis, Emboli


title: 13301358 - Sha a vs RIL 140 a

hyb_protocol: RIL 140 a Cy5 / Sha a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300746 - Sha b vs RIL 140 b

hyb_protocol: RIL 140 b Cy5 / Sha b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC S. aureus INF 952 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.35

value: 15y, when sample taken

value: Black

value: Bacteremia, Osteomyelitis, Pneumonia


title: PBMC S. aureus INF 949 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.34

value: Bacteremia, Osteomyelitis, Suppurative Arthritis


title: PBMC S. aureus INF 954 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.36

value: 13y, when sample taken

value: White

value: Bacteremia, Osteomyelitis, Pyomyositis


title: PBMC S. aureus INF 150 HG-U133B

value: 9y, when sample taken

value: Female

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Myositis


title: PBMC S. aureus INF 205 HG-U133B

value: 7y, when sample taken

value: Hispanic

value: Bacteremia, Pneumonia, Skin/Soft Tissue Abscess


title: PBMC S. aureus INF 944 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.33

value: 6y, when sample taken

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Pyomyositis


title: PBMC Healthy Control INF 941 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.31


title: PBMC S. aureus INF 208 HG-U133B

value: 10y, when sample taken

value: Bacteremia, Osteomyelitis, CNS Abscess, Pneumonia, Emboli

value: Anti-staphylococcal antibiotic


title: PBMC Healthy Control INF 940 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.30

value: Male


title: PBMC S. aureus INF 943 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.32

value: Osteomyelitis, Suppurative Arthritis, Pyomyositis


title: 13300744 - RIL 104 b vs Bay0 b

hyb_protocol: Bay0 b Cy5 / RIL 104 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (shahdara)

value: (boyes et al. plant cell 2001):boyes:6.50

value: arabidopsis thaliana (ril bay-0 x shahdara)


title: PBMC Healthy Control INF 11N HG-U133B

description: Healthy patient.

value: 4y, when sample taken

value: Black


title: 13300743 - Bay0 b vs RIL 104 b

hyb_protocol: RIL 104 b Cy5 / Bay0 b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBMC Healthy Control INF 939 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.29

value: 8y, when sample taken

value: White


title: PBMC S. aureus INF 109 HG-U133B

value: 0.67y, when sample taken

value: Female

value: Bacteremia, Skin/Soft Tissue Abscess


title: 50 passages, biol rep 2

status: Public on May 29 2009

city: Galveston

first: Utpal

last: Pandya

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Biological replicate 2 of 2

hyb_protocol: The Cy3- and Cy5-specific cDNAs were combined and concentrated using concentration filters and hybridized to S. pneumoniae genome microarrays chip obtained from Pathogen Functional Genomics Center (PFGRC) using there protocol.

scan_protocol: Scanned with an Axon 4000B laser scanner.

data_processing: Spot location, array alignment, and background subtraction were assessed with GenePix Pro 4.1. Cy5 and  Cy3 fluorescent intensities were adjusted for local background and normalized to the median intensity of the respective channel in which it was scanned.

organism: Streptococcus pneumoniae

source_name: 50 Passages

label_protocol: The fluorescence-labeled cDNAs were generated through random priming and standard reverse transcription reactions using 2 μg purified RNA in the presence of cyanine dye. Briefly, RNA was heated at 80 °C for 10 min and immediately placed on ice. The RT–PCR consisted of 2 μg RNA, 4 μg random hexamers, 200 units of Super Script II reverse transcriptase (Invitrogen), 1× enzyme reaction buffer, and 500 μM each of dATP, dCTP, dGTP, and dTTP. The reaction was carried out at 42 °C for 2 h and was terminated using 0.5 M NaOH and 50 mM EDTA. RNA was hydrolyzed at 65 °C for 10 min with NaOH and then neutralized with 1 M Tris-HCl, pH 7.5. The cDNAs were purified with a QIAquick 96-well plate PCR purification kit (Qiagen) according to the manufacturer's protocol.

growth_protocol: Bacteria were grown to mid logarithmic phase (OD600 = 0.5) in Todd Hewitt broth (THY) medium at 37°C in  (THY) in a candle extinction jar after passage (1P, 50P, 100P) on blood agar plates.

extract_protocol: An RNeasy mini kit form Qiagen was used for total RNA isolation

treatment_protocol: Serial Passge on blood agar plates

tag: 50 passage strain

source_name: 1 Passage

tag: S. pneumoniae 6304 serotype 4

tag: single passage strain


title: PBMC Healthy Control INF 930 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.25

tag: age

tag: gender

value: Other


title: PBMC Healthy Control INF 927 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.23

value: 2y, when sample taken

value: Hispanic

tag: treatment


title: PBMC Healthy Control INF 935 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.28

value: 9y, when sample taken


title: PBMC S. aureus INF 894 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.13

value: Osteomyelitis, Skin/Soft Tissue Abscess

value: Anti-staphylococcal antibiotic


title: PBMC S. aureus INF 909 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.19

value: 6y, when sample taken

value: Bacteremia, Osteomyelitis, Suppurative Arthritis, Pneumonia


title: PBMC Healthy Control INF 903 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.14

value: 13y, when sample taken


title: PBMC Healthy Control INF 933 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.27

value: Male


title: embryo treated with 1uM AGN193019, biological rep3

city: Seattle

first: Lei

last: Feng

state: WA

address: 1100 Fairview Ave. North, B2-152

department: Basic Science

institute: FHCRC

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Hybridization was performed utilizing the Affymetrix recommended protocol.  15 µg of fragmented biotin-labeled cRNA was combined with hybridization buffer. 200 l (10 µg) of this mix was then placed on the Zebrafish array and hybridized 16 hours at 45ºC at 60 rpm in a GeneChip Hybridization Oven 640.  The arrays were washed and stained with Streptavidin Phycoerythrin (SAPE) using Affymetrix recommended protocols and a fluidics station 450. The wash protocol used was EukGE_WS2v4_450.

scan_protocol: The arrays were scanned using Affymetrix recommended protocols and a GeneChip Scanner 3000 with GCOS 1.2 software.

data_processing: All sample labeling and hybridizations, as well as chip processing and imaging were performed with strict adherence to Affymetrix’s standardized protocols in the FHCRC microarray core facility. A single cycle of target synthesis and labeling was used for all samples. Array normalization was performed using GCRMA (Wu et. al. 2004). Significant changes in expression level were identified using CyberT (Baldi and Long, 2001), a Bayesian t-statistic derived for microarray analysis. Significance was determined by ranking the Bayesian p-values and using a false discovery rate methodology (FDR) to account for multiple testing (Benjamini, 1995). A FDR of 5% was used for the analysis.

organism: Danio rerio

source_name: Danio embryos at 11hpf treated with 1uM AGN193019 from 5.25 hpf

label_protocol: RNA samples were labeled using the Affymetrix recommended protocol which includes a first and second strand cDNA synthesis from total RNA, followed by in vitro transcription (IVT) using the ENZO IVT kit to incorporate biotin into the synthesized cRNA. The biotin-labeled cRNA was purified over a column and quality was checked using the bioanalyzer and spectrophotometer.  20 µg of biotin-labeled cRNA was then fragmented, 15 µg was reserved for the hybridization and the remainder was used in quality control analysis on the bioanalyzer.

growth_protocol: Zebrafish embryos of the *ABxWIK hybrid background were maintained at 28.5˚C under standard conditions prior to treatment. Embryos were dechorionated enzymatically before treatment and were kept in agarose-coated dishes during treatment.

extract_protocol: RNAwiz extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: When embryos reached the appropriate stage (5.25 hours post fertilization (hpf) for AGN193109 (Allergan, Irvine, CA), DMSO (Sigma), and 6.5 hpf for atRA [all-trans Retinoic Acid] (Sigma), they were transferred to agarose-coated dishes containing the appropriate amount of drug or comparable solvent. Embryos used for the microarray analysis were treated with 0.33 mM atRA, 10 mM AGN 193109, 1 mM AGN 193109 or 2% DMSO, all diluted 1:50 from stock solutions in DMSO. At the end of treatment, embryos were rinsed once in embryo media prior to RNA isolation.

tag: tissue

value: dechorionated embryo

tag: genotype

value: wt incross from AB/Wik hybrid parents

value: embryos at 11hpf


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 2A

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: The labeling procedure uses equal quantities of RNA from adequate Zn and Zn-limited cultures.

hyb_protocol: The Cy3-dCTP-labeled sample was mixed with the Cy5-dCTP-labeled sample and re-suspended in 120 microlitres salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 1× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 500 × g for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner.  The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 5.0 and GeneSight, version 4.0).

data_processing: Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 or Cy5/Cy3 (test/reference) fluorescent ratios were calculated from the normalized values.

organism: Escherichia coli

source_name: Steady-state continuously-cultured control samples in the presence of adequate Zn

label_protocol: RNA (15-20 µg) was annealed to 9 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC.  This was supplemented with 4 microlitres of 5× First-strand buffer (Invitrogen), 2 microlitres dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 2 microlitres 0.1 M DTT, 2 microlitres 1 mM Cy3 (Perkin Elmer) and 1 microlitre Superscript II reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 2 hours.  The reaction was terminated by the addition of NaOH (5 microlitres of 1M) and HCl (5 microlitres of 1M) before the addition of TE buffer (200 microlitres).  Labeled cDNA was purified using a Qiaquick purification kit (Qiagen).

extract_protocol: After 50 hours, samples (10 ml) were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf).

tag: Steady-state continuously-cultured MG1655 in the presence of adequate Zn

source_name: Steady-state continuously-cultured experiment samples in the total absence of Zn

label_protocol: RNA (15-20 µg) was annealed to 9 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC.  This was supplemented with 4 microlitres of 5× First-strand buffer (Invitrogen), 2 microlitres dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 2 microlitres 0.1 M DTT, 2 microlitres 1 mM Cy5 (Perkin Elmer) and 1 microlitre Superscript II reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 2 hours.  The reaction was terminated by the addition of NaOH (5 microlitres of 1M) and HCl (5 microlitres of 1M) before the addition of TE buffer (200 microlitres).  Labeled cDNA was purified using a Qiaquick purification kit (Qiagen).

tag: Steady-state continuously-cultured MG1655 in the total absence of Zn


title: PBMC S. aureus INF 910 Illumina Human6

scan_protocol: SentrixScanVersion 2.3.0.20

value: 5y, when sample taken

value: Black

value: Osteomyelitis, Suppurative Arthritis


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 1A

source_name: Steady-state continuously-cultured experiment samples in total absence of Zn


title: embryo treated with 1uM AGN193019, biological rep4


title: PBMC Healthy Control INF 929 Illumina Human6

description: Healthy patient.

scan_protocol: SentrixScanVersion 2.3.0.24

value: 11y, when sample taken

value: Female


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 1B


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 2B


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 3A


title: embryo treated with 1uM AGN193019, biological rep2


title: Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 3B


title: embryo treated with 1uM AGN193019, biological rep1


title: Spleen 72H-1

city: Porto

first: Didier

last: Cabanes

state: Porto

address: rua do Campo Alegre, 823

country: Portugal

institute: IBMC

hyb_protocol: Macroarrays were pre-hybridized in roller bottles with 10 ml of a hybridization solution containing 5X SSPE (1X SSPE is 0.18 M NaCl, 10 mM NaH2PO4 and 1 mM EDTA pH7.7), 2% SDS, 1X Denhardt’s reagent (Sigma), 100 ug/ml of sonicated salmon sperm DNA for 1h at 65oC. Hybridizations were performed overnight at 65oC with 5 ml of fresh hybridization solution containing the labeled cDNA. After hybridization macroarrays were washed twice for 5 min at room temperature and twice for 20 min at 65oC with a washing solution (0.5X SSPE, 0.2% SDS).

scan_protocol: The macroarrays were then exposed to a phosphoimager screen and scanned with the Typhoon phosphoimager (Pharmacia-Amersham). Two hybridizations for each independent RNA extraction were performed. In total, a set of 4 macroarrays was used for each strain. Hybridized arrays were scanned using the Typhoon 9400 phosphoimager (Amersham Biosciences). The signal intensity was quantified using the ArrayVision software (Imaging Research). The intensity was measured in arbitrary units using the ARMdens measure.

data_processing: The intensity of each spot was normalized according to the median value of the total intensities of all spots on each array. The global background was calculated from the median intensity of 610 “no-DNA” spots homogeneously distributed throughout the membrane.

organism: Listeria monocytogenes EGD-e

source_name: Listeria monocytogenes EGDe from infected mouse spleen 72H post infection

label_protocol: Total RNA (1ug) was mixed with 6 ul of 5X AMV reverse transcriptase buffer (Roche), 3 ul of a mixture of dATP, dGTP, dTTP (10 mM), 5 ug of random hexamers (Primer Random p(dN)6, Roche) and DEPC-treated water to a final volume of 21 ul. The mixture was heated at 90oC for 2 min and cooled to 42oC before addition of 3 ul of alpha-33P dCTP (20 uCi) and 2 ul (50U/ul) of AMV reverse transcriptase (Roche). The mixture was incubated for 2 h at 42oC. A column was used for the removal of unincorporated nucleotides according to the manufacturer’s instructions (QIAquick Nucleotide Removal Kit, QIAgen). The obtained cDNA was denaturated by heating at 99oC for 5 min just before hybridization.

extract_protocol: At 72h post-infection, mice were sacrificed and dissected. The livers and spleens were harvested and immediately frozen in liquid nitrogen. The organs were stored at –80ºC. Prior to RNA isolation, the organs were thawed on ice and homogenized in 20 ml of an ice-cold solution composed of 0.2M sucrose/0.01% SDS. The homogenate was gently centrifuged for 20 min at 300 rpm and filtered to remove large tissue debris. The tissue suspension was centrifuged for 20 min at 4000 rpm to pellet the bacteria. Centrifugations were performed at 4ºC. Bacteria were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.


title: embryo treated with 10uM AGN193019, biological rep4

source_name: Danio embryos at 11hpf treated with 10uM AGN193019 from 5.25 hpf


title: Spleen 24H-2

source_name: Listeria monocytogenes EGDe mouse spleen 24H post infection

extract_protocol: At 24h post-infection, mice were sacrificed and dissected. The livers and spleens were harvested and immediately frozen in liquid nitrogen. The organs were stored at –80ºC. Prior to RNA isolation, the organs were thawed on ice and homogenized in 20 ml of an ice-cold solution composed of 0.2M sucrose/0.01% SDS. The homogenate was gently centrifuged for 20 min at 300 rpm and filtered to remove large tissue debris. The tissue suspension was centrifuged for 20 min at 4000 rpm to pellet the bacteria. Centrifugations were performed at 4ºC. Bacteria were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.


title: embryo treated with 10uM AGN193019, biological rep2


title: Spleen 24H-1

source_name: Listeria monocytogenes EGDe from infected mouse spleen 24H post infection


title: embryo treated with 10uM AGN193019, biological rep3


title: BHI-1

source_name: Listeria monocytogenes EGDe in BHI in exponential growth phase

extract_protocol: Cells were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.

tag: Listeria monocytogenes EGDe in BHI at 37ºC in exponential growth phase


title: embryo treated with 10uM AGN193019, biological rep1


title: Spleen 48H-1

source_name: Listeria monocytogenes EGDe from infected mouse spleen 48H post infection

extract_protocol: At 48h post-infection, mice were sacrificed and dissected. The livers and spleens were harvested and immediately frozen in liquid nitrogen. The organs were stored at –80ºC. Prior to RNA isolation, the organs were thawed on ice and homogenized in 20 ml of an ice-cold solution composed of 0.2M sucrose/0.01% SDS. The homogenate was gently centrifuged for 20 min at 300 rpm and filtered to remove large tissue debris. The tissue suspension was centrifuged for 20 min at 4000 rpm to pellet the bacteria. Centrifugations were performed at 4ºC. Bacteria were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.


title: BHI-2


title: Spleen 48H-2

tag: Listeria monocytogenes EGDe from infected mouse spleen 48H post infection


title: Spleen 72H-2

tag: Listeria monocytogenes EGDe from infected mouse spleen 72H post infection


title: embryo treated with 0.33uM RA, biological rep4

source_name: Danio embryos at 11hpf treated with 0.33uM RA from 6.5 hpf


title: embryo treated with DMSO, biological rep4

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: Danio embryos at 11hpf treated with 2% DMSO from 5.25 hpf


title: embryo treated with 0.33uM RA, biological rep2


title: embryo treated with DMSO, biological rep3


title: embryo treated with 0.33uM RA, biological rep1


title: 50 passages, biol rep 1

description: Biological replicate 1 of 2


title: 100 passages, biol rep 1

description: Biological replicate 1 of 2

source_name: 100 Passages

tag: 100 passage strain


title: embryo treated with DMSO, biological rep1


title: 100 passages, biol rep 2

description: Biological replicate 2 of 2


title: embryo treated with DMSO, biological rep2


title: PES_252_rep3

status: Public on May 28 2009

city: SAINT PAUL

first: John

middle: W

last: Gronwald

state: MN

address: 1991 UPPER BUFORD CIRCLE

institute: USDA-ARS

description: Gene expression data from post-elongation stem of alfalfa genotype 252.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Medicago Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Cel files were analyzed by GCOS1.4 with scale factor of 1.0, without normalization.

organism: Medicago sativa

source_name: post-elongation stem from genotype 252

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The alfalfa clonal lines 252 and 1283 were propagated from cuttings and grown in the greenhouse. The greenhouse experiments consisted of three replicates arranged in a randomized complete block design. There were eight plants of each clone, in individual pots, in each replicate.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: Genotype 252.

tag: The internodes immediately below the transition internode.


title: PES_252_rep2


title: PES_252_rep1


title: ES_1283_rep3

description: Gene expression data from elongating stem of alfalfa genotype 1283.

source_name: elongating stem from genotype 1283

tag: Genotype 1283.

tag: The internodes immediately above the transition internode.


title: PES_1283_rep1

description: Gene expression data from post-elongation stem of alfalfa genotype 1283.

source_name: post-elongation stem from genotype 1283


title: embryo treated with 0.33uM RA, biological rep3


title: ES_252_rep3

description: Gene expression data from elongating stem of alfalfa genotype 252.

source_name: elongating stem from genotype 252


title: ES_1283_rep2


title: PES_1283_rep3


title: PES_1283_rep2


title: ES_1283_rep1


title: ES_252_rep2


title: ES_252_rep1


title: refF04

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: pool of 10 female individuals

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: CNAG 2.0 and Affymetrix Genotypic Console 2.1

source_name: Peripheral blood

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

value: female

tag: sample

value: control sample

value: Peripheral blood


title: refF05

description: pool of 10 female individuals


title: refF01

description: pool of 10 female individuals